Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_012850596.1 TCUR_RS01030 class II fructose-bisphosphate aldolase
Query= BRENDA::P9WQA3 (344 letters) >NCBI__GCF_000024385.1:WP_012850596.1 Length = 340 Score = 483 bits (1244), Expect = e-141 Identities = 240/342 (70%), Positives = 276/342 (80%), Gaps = 3/342 (0%) Query: 1 MPIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFG 60 MPIATPEVYAEML +AK +A+PAIN TSS+T+NAA++GFA+A SDGIIQ STGGAE+ Sbjct: 1 MPIATPEVYAEMLDRAKAEGFAYPAINVTSSQTLNAALRGFAEAESDGIIQISTGGAEYL 60 Query: 61 SGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKG 120 SG VKDMVTGAVA AE+ V+AAKYPVN+ALHTDHCPK+KLD ++RPL+ IS +RV+KG Sbjct: 61 SGTAVKDMVTGAVAFAEYARVVAAKYPVNIALHTDHCPKEKLDGFMRPLVKISQERVAKG 120 Query: 121 GNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKL 180 PLFQSHMWDGSAV + ENL IA ELL+ A+ I+E+EIGVVGGEEDG+ EINEKL Sbjct: 121 QEPLFQSHMWDGSAVELRENLQIAAELLEECVKARTIMEMEIGVVGGEEDGIVGEINEKL 180 Query: 181 YTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGL 240 YT+ ED T EA+G GE G+Y+LAATFGNVHGVYKPG+VKLRP +L + Q+ AK G Sbjct: 181 YTTTEDALATAEAVGVGEKGRYILAATFGNVHGVYKPGHVKLRPQVLKEIQEAVGAKYG- 239 Query: 241 PADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLK 300 KPFD VFHGGSGS EI EA+ YGV+KMN+DTDTQYAFTRPIA HMF NYDGVLK Sbjct: 240 --KDKPFDLVFHGGSGSTLEEIREAVSYGVIKMNIDTDTQYAFTRPIADHMFRNYDGVLK 297 Query: 301 VDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSL 342 VDGEVG KK YDPRSY K AEA M+ RVVQAC DL AGK L Sbjct: 298 VDGEVGNKKTYDPRSYGKAAEAGMAARVVQACQDLMSAGKKL 339 Lambda K H 0.316 0.133 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 395 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 344 Length of database: 340 Length adjustment: 29 Effective length of query: 315 Effective length of database: 311 Effective search space: 97965 Effective search space used: 97965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_012850596.1 TCUR_RS01030 (class II fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01520.hmm # target sequence database: /tmp/gapView.1212.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01520 [M=357] Accession: TIGR01520 Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-135 438.0 0.7 1.4e-135 437.9 0.7 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012850596.1 TCUR_RS01030 class II fructose-b Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012850596.1 TCUR_RS01030 class II fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.9 0.7 1.4e-135 1.4e-135 9 355 .. 3 336 .. 1 338 [. 0.98 Alignments for each domain: == domain 1 score: 437.9 bits; conditional E-value: 1.4e-135 TIGR01520 9 vilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaek 77 ++++e++a++++ ak e fa Painv+ss+t+naal+++++a+s++i+q+s+gga++++G vkd lcl|NCBI__GCF_000024385.1:WP_012850596.1 3 IATPEVYAEMLDRAKAEGFAYPAINVTSSQTLNAALRGFAEAESDGIIQISTGGAEYLSGTAVKD---- 67 789**************************************************************.... PP TIGR01520 78 aasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllp.yvdglleadekyfkkegkPlfsshmldlse 145 +++Ga+a aey r++a+ky+v+++lhtdhC+k++l+ ++++l+++++++++k+++Plf+shm+d+s+ lcl|NCBI__GCF_000024385.1:WP_012850596.1 68 --MVTGAVAFAEYARVVAAKYPVNIALHTDHCPKEKLDgFMRPLVKISQERVAKGQEPLFQSHMWDGSA 134 ..9****************************************************************** PP TIGR01520 146 epieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelsk.ispk 213 + + en++ia ++l+ k+ i+e+eiG++GGeedG+ e + e+lyt+ ed + e++ ++++ lcl|NCBI__GCF_000024385.1:WP_012850596.1 135 VELRENLQIAAELLEECVKARTIMEMEIGVVGGEEDGIVGEIN--EKLYTTTEDALATAEAVGVgEKGR 201 *****************************************99..9***************99889*** PP TIGR01520 214 fsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvv 282 + +aa+fGnvhGvykpG vklrP++l++ qe v +k g + kp+++vfhGGsGst eei+ea+syGv+ lcl|NCBI__GCF_000024385.1:WP_012850596.1 202 YILAATFGNVHGVYKPGHVKLRPQVLKEIQEAVGAKYGKD--KPFDLVFHGGSGSTLEEIREAVSYGVI 268 *************************************987..*************************** PP TIGR01520 283 kvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleel 351 k+n+dtdtqya++++i+d++++n+d +++++G e++nkk+ydPr++ ++ae+ m arv++a+++l lcl|NCBI__GCF_000024385.1:WP_012850596.1 269 KMNIDTDTQYAFTRPIADHMFRNYDGVLKVDG-----EVGNKKTYDPRSYGKAAEAGMAARVVQACQDL 332 ********************************.....9******************************9 PP TIGR01520 352 nain 355 +++ lcl|NCBI__GCF_000024385.1:WP_012850596.1 333 MSAG 336 8876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (340 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.34 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory